These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
4. Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations. Uehara S; Tanaka S J Chem Inf Model; 2017 Apr; 57(4):742-756. PubMed ID: 28388074 [TBL] [Abstract][Full Text] [Related]
5. EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation. Yanagisawa K; Moriwaki Y; Terada T; Shimizu K J Chem Inf Model; 2021 Jun; 61(6):2744-2753. PubMed ID: 34061535 [TBL] [Abstract][Full Text] [Related]
6. Excluded volume contribution to cosolvent-mediated modulation of macromolecular folding and binding reactions. Chalikian TV Biophys Chem; 2016 Feb; 209():1-8. PubMed ID: 26569082 [TBL] [Abstract][Full Text] [Related]
7. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. Cimermancic P; Weinkam P; Rettenmaier TJ; Bichmann L; Keedy DA; Woldeyes RA; Schneidman-Duhovny D; Demerdash ON; Mitchell JC; Wells JA; Fraser JS; Sali A J Mol Biol; 2016 Feb; 428(4):709-719. PubMed ID: 26854760 [TBL] [Abstract][Full Text] [Related]
8. Parameter choice matters: validating probe parameters for use in mixed-solvent simulations. Lexa KW; Goh GB; Carlson HA J Chem Inf Model; 2014 Aug; 54(8):2190-9. PubMed ID: 25058662 [TBL] [Abstract][Full Text] [Related]
9. Cosolvent-Enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-Based Drug Design. Schmidt D; Boehm M; McClendon CL; Torella R; Gohlke H J Chem Theory Comput; 2019 May; 15(5):3331-3343. PubMed ID: 30998331 [TBL] [Abstract][Full Text] [Related]
10. Molecular Dynamics Simulation and Prediction of Druggable Binding Sites. Feng T; Barakat K Methods Mol Biol; 2018; 1762():87-103. PubMed ID: 29594769 [TBL] [Abstract][Full Text] [Related]
11. Solvents to Fragments to Drugs: MD Applications in Drug Design. Defelipe LA; Arcon JP; Modenutti CP; Marti MA; Turjanski AG; Barril X Molecules; 2018 Dec; 23(12):. PubMed ID: 30544890 [TBL] [Abstract][Full Text] [Related]
12. Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches. Bansia H; Mahanta P; Yennawar NH; Ramakumar S J Chem Inf Model; 2021 Mar; 61(3):1322-1333. PubMed ID: 33570386 [TBL] [Abstract][Full Text] [Related]
13. Accelerated Ligand-Mapping Molecular Dynamics Simulations for the Detection of Recalcitrant Cryptic Pockets and Occluded Binding Sites. Tze-Yang Ng J; Tan YS J Chem Theory Comput; 2022 Mar; 18(3):1969-1981. PubMed ID: 35175753 [TBL] [Abstract][Full Text] [Related]
14. Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth. Lal Gupta P; Carlson HA J Chem Theory Comput; 2022 Jun; 18(6):3829-3844. PubMed ID: 35533286 [TBL] [Abstract][Full Text] [Related]
15. Divide and Conquer. Pocket-Opening Mixed-Solvent Simulations in the Perspective of Docking Virtual Screening Applications for Drug Discovery. Sabanés Zariquiey F; Jacoby E; Vos A; van Vlijmen HWT; Tresadern G; Harvey J J Chem Inf Model; 2022 Feb; 62(3):533-543. PubMed ID: 35041430 [TBL] [Abstract][Full Text] [Related]
16. Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations. Ghanakota P; DasGupta D; Carlson HA J Chem Inf Model; 2019 May; 59(5):2035-2045. PubMed ID: 31017411 [TBL] [Abstract][Full Text] [Related]
17. Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents. Stepankova V; Khabiri M; Brezovsky J; Pavelka A; Sykora J; Amaro M; Minofar B; Prokop Z; Hof M; Ettrich R; Chaloupkova R; Damborsky J Chembiochem; 2013 May; 14(7):890-7. PubMed ID: 23564727 [TBL] [Abstract][Full Text] [Related]
18. Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics. Kimura SR; Hu HP; Ruvinsky AM; Sherman W; Favia AD J Chem Inf Model; 2017 Jun; 57(6):1388-1401. PubMed ID: 28537745 [TBL] [Abstract][Full Text] [Related]
19. PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations. Martinez-Rosell G; Lovera S; Sands ZA; De Fabritiis G J Chem Inf Model; 2020 Apr; 60(4):2314-2324. PubMed ID: 32175736 [TBL] [Abstract][Full Text] [Related]